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Yorodumi- PDB-5lt1: nucleotide-free kinesin-1 motor domain T92V mutant, P21 crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lt1 | ||||||||||||
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Title | nucleotide-free kinesin-1 motor domain T92V mutant, P21 crystal form | ||||||||||||
Components | Kinesin-like protein | ||||||||||||
Keywords | MOTOR PROTEIN / Kinesin motor domain / ADP dissociation / nucleotide-free | ||||||||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / natural killer cell mediated cytotoxicity / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / mitochondrion transport along microtubule / ciliary rootlet / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / centriolar satellite / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / phagocytic vesicle / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / axon guidance / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / microtubule binding / microtubule / vesicle / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å | ||||||||||||
Authors | Cao, L. / Gigant, B. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: The structural switch of nucleotide-free kinesin. Authors: Cao, L. / Cantos-Fernandes, S. / Gigant, B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lt1.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lt1.ent.gz | 213.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lt1_validation.pdf.gz | 461.9 KB | Display | wwPDB validaton report |
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Full document | 5lt1_full_validation.pdf.gz | 465.6 KB | Display | |
Data in XML | 5lt1_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 5lt1_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/5lt1 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/5lt1 | HTTPS FTP |
-Related structure data
Related structure data | 5lt0C 5lt2C 5lt3C 5lt4C 1bg2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36274.773 Da / Num. of mol.: 2 / Mutation: C7S, C65A, T92V, C168A, C174S, C294A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6P164, UniProt: P33176*PLUS #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-SR / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na-Acetate pH 4.5-5.5 23% PEG 4000 0.2 M Ammonium Sulfate 0.1 M SrCl2 PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→44 Å / Num. obs: 53434 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.18 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.18 / Net I/σ(I): 6.5 |
Reflection shell | Rrim(I) all: 1.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BG2 Resolution: 1.949→43.353 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.949→43.353 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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